Federer reached the landmark with a ruthless 6-4, 6-4 dismantling of Greece's Stefanos Tsitsipas in the Dubai Championship final, his eighth trophy at the Gulf event.
His 100th title comes 18 years after he captured his first in Milan.
Federer, the winner of a record 20 Grand Slam titles, said that he's not particularly targeting the 109-mark of Connors.
“A lot of people always ask me about, 'Are you going to go for 109?'”, said Federer.
“To answer the question is not easy. Winning five matches in six days or five matches in five days, it takes a different type of fitness.
“You can play a great tournament, play a brutal semi, you get unlucky sometimes with the schedule, whatever it may be.
He added: “That's why you have to be fit on many fronts: mentally, physically; you have to be able to beat different types of players: beat them all on successive days.”
Connors, who set his record during his glory years in the 1970s and 1980s, took to Twitter to congratulate the Swiss star.
“Welcome to the 'Triple Digit' tournament victory club @rogerfederer – I've been a bit lonely – glad to have the company,” wrote the American.
Welcome to the “ Triple Digit” tournament victory club @rogerfederer — I’ve been a bit lonely- glad to have the company !!!
— Jimmy Connors (@JimmyConnors) March 2, 2019
Federer, who remains a long way back from the all-time mark of 167 titles set in the women's game by Martina Navratilova, said that his two-decade longevity was key to the title century.
“It's a deep satisfaction, an immediate one. A lot of people always emphasise all the Slams, but I play on the ATP Tour. This is where I've won so many of them. Been around for so long,” he added.
“I don't rest between Slams all the time, like people think I might be. I think this number proves that. I think that's why this was a very exciting week for me.”
The Swiss star will have little time to contemplate achieving yet another record with Indian Wells in California, next on the agenda for the first Masters of the season.
“I didn't come here expecting I was going to win, to be quite honest. I hadn't played since Australia,” explained Federer who had been defeated by Tsitsipas in the fourth round at the Australian Open in January.
“I'm just happy on all fronts how my game has progressed, how well I played in the final, winning the eighth Dubai title, winning the 100th.
“So many magical things going on. I'm very, very happy right now.”
Federer's 99th trophy had come last October at his home event in Basel.
He missed out on the century at the Paris Masters, the ATP Finals in London and then at Melbourne.
On Saturday, the second seed was untouchable throughout much of the 69-minute final as he gained revenge for his shock Australian Open defeat by the 11th-ranked Greek.
Tsitsipas, who will become the first Greek to ever reach the world's top 10 on Monday, paid tribute to his opponent.
“100 (titles) is just completely insane — I'd be happy with 100 wins. Seriously, I'm trying to get there,” he said.
Tsitsipas admitted he had few chances in the rout.
“He was very aggressive, didn't give me any time today. I was expecting it,
for him to be a little more aggressive.
“He just seemed like having control over everything he was doing, taking the ball super early, on the rise, giving me no time to prepare.
“It felt like he was controlling everything on his own terms.”
Tsitsipas saw the end of an eight-match winning streak as he arrived in the Gulf with the Marseille title from last weekend.
Federer broke in the opening game of the final, but had to battle to claim the opening set.
Tsitsipas saved three set points in the final game before Federer — who faced two break points — finished off the set as the Greek returned wide.
In the second set, a break in the penultimate game for 5-4 and a service hold a game later were enough as Tsitsipas put a forehand into the net.